[med-svn] r3439 - trunk/packages/seaview/trunk/debian

Charles Plessy plessy at alioth.debian.org
Wed May 27 13:22:24 UTC 2009 

Author: plessy
Date: 2009-05-27 13:22:23 +0000 (Wed, 27 May 2009)
New Revision: 3439

Removed:
   trunk/packages/seaview/trunk/debian/README.Debian
Modified:
   trunk/packages/seaview/trunk/debian/changelog
   trunk/packages/seaview/trunk/debian/control
   trunk/packages/seaview/trunk/debian/copyright
   trunk/packages/seaview/trunk/debian/seaview.1
   trunk/packages/seaview/trunk/debian/seaview.1.xml
Log:
Uploaded to non-free :(


Deleted: trunk/packages/seaview/trunk/debian/README.Debian
===================================================================
--- trunk/packages/seaview/trunk/debian/README.Debian	2009-05-27 04:24:24 UTC (rev 3438)
+++ trunk/packages/seaview/trunk/debian/README.Debian	2009-05-27 13:22:23 UTC (rev 3439)
@@ -1,18 +0,0 @@
-SeaView for Debian
-------------------
-
-The version of SeaView packaged for Debian has the following modifications:
-
-- It uses by default the program "Muscle" for re-aligning residues, as ClustalW
-  is not free enough to be distributed in Debian.
-
-- It outputs the alignments in PostScript format and not in PDF, as the
-  software for PDF support (PDFlib) is not free enough to be distributed in
-  Debian.
-
-- It uses the default X terminal emulator instead of Xterm, when re-aligning
-  residues. You can check which alternative you are using with the following
-  command:
-    /usr/sbin/update-alternatives --display x-terminal-emulator
-
- -- Charles Plessy <charles-debian-nospam at plessy.org>  Thu, 28 Sep 2006 12:13:53 +0900

Modified: trunk/packages/seaview/trunk/debian/changelog
===================================================================
--- trunk/packages/seaview/trunk/debian/changelog	2009-05-27 04:24:24 UTC (rev 3438)
+++ trunk/packages/seaview/trunk/debian/changelog	2009-05-27 13:22:23 UTC (rev 3439)
@@ -1,12 +1,14 @@
-seaview (1:4.0-1) UNRELEASED; urgency=low
+seaview (1:4.0-1) unstable; urgency=low
 
-  DO NOT UPLOAD: contains non-free files: csrc/dnapars.c and csrc/protpars.c
-
-  * New upstream version that computes and draws parsimony, distance and PhyML
-    phylogenetic trees.
+  * New upstream version
+    - Computes and draws parsimony, distance and PhyML phylogenetic trees.
+    - This new version unfortunately uses non-free files, and has therefore been
+      removed from Debian, but is distributed in the ‘non-free’ section of its
+      archive as a service its users.
   * debian/control:
+    - Changed section to non-free/science.
     - Build-Depends on libxft-dev and libxext-dev.
-    - Recommends phyml and muscle.
+    - Recommends phyml, muscle and clustalw.
     - Dropped dependency on xterm.
     - checked package conformance with Policy 3.8.1.
     - Updated description and removed reference from it.
@@ -17,6 +19,7 @@
       debian/rules instead.
     - 40-seaview_align.sh-newline.patch, seaview_align-full_path.patch:
       seaview_align.sh was removed upstream.
+  * debian/README.Debian deleted as well (obsolete).
   * debian/rules:
     - Makes `seaview' instead of `seaviewps' as (non-free) PDF support is not
       default anymore.
@@ -31,10 +34,11 @@
   * debian/copyright:
     - Incremented year and version.
     - Link to the precise versions of the GNU GPL and LGPL.
+    - Added the necessary disclaimers because SeaView became non-free.
   * Updated the manpage (debian/seaview.1*).
   * Registered the new help file with doc-base (debian/seaview.doc-base.help).
 
- -- Charles Plessy <plessy at debian.org>  Sun, 17 May 2009 09:22:35 +0900
+ -- Charles Plessy <plessy at debian.org>  Wed, 27 May 2009 08:07:40 +0900
 
 seaview (1:3.2-1) unstable; urgency=low
 

Modified: trunk/packages/seaview/trunk/debian/control
===================================================================
--- trunk/packages/seaview/trunk/debian/control	2009-05-27 04:24:24 UTC (rev 3438)
+++ trunk/packages/seaview/trunk/debian/control	2009-05-27 13:22:23 UTC (rev 3439)
@@ -1,5 +1,5 @@
 Source: seaview
-Section: science
+Section: non-free/science
 Priority: optional
 Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 DM-Upload-Allowed: yes
@@ -13,8 +13,7 @@
 Package: seaview
 Architecture: any
 Depends: ${shlibs:Depends}, ${misc:Depends}
-Recommends: muscle, phyml
-Suggests: clustalw
+Recommends: clustalw, muscle, phyml
 Description: Multiplatform interface for sequence alignment and phylogeny
  SeaView reads and writes various file formats (NEXUS, MSF, CLUSTAL, FASTA,
  PHYLIP, MASE, Newick) of DNA and protein sequences and of phylogenetic trees.

Modified: trunk/packages/seaview/trunk/debian/copyright
===================================================================
--- trunk/packages/seaview/trunk/debian/copyright	2009-05-27 04:24:24 UTC (rev 3438)
+++ trunk/packages/seaview/trunk/debian/copyright	2009-05-27 13:22:23 UTC (rev 3439)
@@ -1,10 +1,43 @@
 Format: Machine-readable license summary, see http://dep.debian.net/deps/dep5/
+
 Name: SeaView
 Contact: Manolo Gouy <mgouy at biomserv.univ-lyon1.fr>
 Source: ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_4.0.tar.gz
+Disclamer:
+ This package is not part of the Debian operating system. The seaview source
+ and binary Debian packages are part of the “non-free” area in our archive. The
+ packages in this area are not part of the Debian system, although they have
+ been configured for use with Debian. We nevertheless support the use of the
+ seaview source and binary Debian pacakges and provide infrastructure for
+ non-free packages (such as our bug tracking system and mailing lists). The
+ licences of SeaView do not forbid Debian from using autobuilders to create
+ binary packages.
 
 Copyright: 1996-2009 Manolo Gouy <mgouy at biomserv.univ-lyon1.fr>
-License: GPL-2+
+License: GPL-2+ with PHYLIP exemption.
+ This program, except where indicated, is free software; 
+ you can redistribute it and/or
+ modify it under the terms of the GNU General Public
+ License as published by the Free Software Foundation; either
+ version 2 of the License, or (at your option) any later version.
+ .
+ Two files (dnapars.c and protpars.c) have a distinct copyright
+ which authorizes distribution that does not generate revenue.
+ .
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ General Public License for more details.
+ .
+ A copy of the GNU General Public License is available
+ from http://www.gnu.org/licenses/gpl.txt or by mail from the Free Software
+ Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ USA.
+Comment: On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in `/usr/share/common-licenses/GPL-2'.
+Comment: Manolo Gouy confirmed to Charles Plessy that SeaView provides a
+ similar exemption regarding the files dnapars.c and protpars.c originating from
+ the PHYLIP phylogeny package, see below.
 Comment: If you use SeaView in a published work, please cite the following reference:
  Galtier, N., Gouy, M. and Gautier, C. (1996) SeaView and Phylo_win, two graphic
  tools for sequence alignment and molecular phylogeny. Comput. Applic. Biosci.,
@@ -12,15 +45,65 @@
 
 Files: csrc/bionj.c, csrc/phyml_util.h
 Copyright: © Stephane Guindon. Oct 2003 onward
-License: GPL-2+
+License: GPL-2+ with PHYLIP exemption.
+ This program is free software; you can redistribute it and/or modify it under the terms of the 
+ GNU General Public License as published by the Free Software Foundation; either version 2 of 
+ the License, or (at your option) any later version.
+ . 
+ This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without 
+ even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 
+ General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License along with this program; if not, 
+ see <http://www.gnu.org/licenses>.
+ .
+ Linking PHYML statically or dynamically with other modules is making a combined work based on PHYML. 
+ Thus, the terms and conditions of the GNU General Public License cover the whole combination.
+ .
+ In addition, as a special exception, the copyright holders of PHYML give you permission to combine 
+ PHYML with free software programs or libraries that are released under the GNU LGPL and with code 
+ included in the standard release of PHYLIP under the University of Washington license (or modified 
+ versions of such code, with unchanged license). You may copy and distribute such a system following 
+ the terms of the GNU GPL for PHYML and the licenses of the other code concerned.
+ .
+ Note that people who make modified versions of PHYML are not obligated to grant this special exception 
+ for their modified versions; it is their choice whether to do so. The GNU General Public License gives 
+ permission to release a modified version without this exception; this exception also makes it possible 
+ to release a modified version which carries forward this exception.
 
 Files: csrc/dnapars.c, csrc/protpars.c
- THESE FILES ARE NON-FREE, DO NOT UPLOAD THIS PACKAGE.
+License:
+ (c) Copyright 1980-2008. University of Washington. All rights reserved. Permission is 
+ granted to reproduce, perform, and modify these programs and documentation files. 
+ Permission is granted to distribute or provide access to these programs provided 
+ that this copyright notice is not removed, the programs are not integrated with or 
+ called by any product or service that generates revenue, and that your distribution 
+ of these documentation files and programs are free. Any modified versions of these 
+ materials that are distributed or accessible shall indicate that they are based on 
+ these programs. Institutions of higher education are granted permission to 
+ distribute this material to their students and staff for a fee to recover 
+ distribution costs. Permission requests for any other distribution of these 
+ program should be directed to  license (at) u.washington.edu . 
 
 Files: FL/*
 Copyright: © 2004 Greg Ercolano
            © 2005 Nathan Vander Wilt 
 License: LGPL-2+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Library General Public
+ License as published by the Free Software Foundation; either
+ version 2 of the License, or (at your option) any later version.
+ .
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ Library General Public License for more details.
+ .
+ You should have received a copy of the GNU Library General Public
+ License along with this library; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston MA  02110-1301 USA
+Comment: On Debian systems, the complete text of the GNU Lesser General
+ Public License version 2 can be found in `/usr/share/common-licenses/LGPL-2'.
 
 Files: debian/*
 Copyright: © 1999 Stephane Bortzmeyer <bortzmeyer at debian.org>
@@ -36,37 +119,3 @@
 	   © 2006-2009 Charles Plessy <charles-debian-nospam at plessy.org>
 License: unknown
  Please treat the contributions of Charles Plessy as if they were in the public domain.
-
-License: GPL-2+
- This package is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 2 of the License, or
- (at your option) any later version.
- .
- This package is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- GNU General Public License for more details.
- .
- You should have received a copy of the GNU General Public License
- along with this package; if not, write to the Free Software
- Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
-Comment: On Debian systems, the complete text of the GNU General
- Public License version 2 can be found in `/usr/share/common-licenses/GPL-2'.
-
-License: LGPL-2+
- This library is free software; you can redistribute it and/or
- modify it under the terms of the GNU Library General Public
- License as published by the Free Software Foundation; either
- version 2 of the License, or (at your option) any later version.
- .
- This library is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- Library General Public License for more details.
- .
- You should have received a copy of the GNU Library General Public
- License along with this library; if not, write to the Free Software
- Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston MA  02110-1301 USA
-Comment: On Debian systems, the complete text of the GNU Lesser General
- Public License version 2 can be found in `/usr/share/common-licenses/LGPL-2'.

Modified: trunk/packages/seaview/trunk/debian/seaview.1
===================================================================
--- trunk/packages/seaview/trunk/debian/seaview.1	2009-05-27 04:24:24 UTC (rev 3438)
+++ trunk/packages/seaview/trunk/debian/seaview.1	2009-05-27 13:22:23 UTC (rev 3439)
@@ -1,11 +1,11 @@
 .\"     Title: SEAVIEW
 .\"    Author: Manolo Gouy <mgouy at biomserv.univ-lyon1.fr>
 .\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\"      Date: 05/17/2009
+.\"      Date: 05/27/2009
 .\"    Manual: Seaview Manual
 .\"    Source: seaview 4.0
 .\"
-.TH "SEAVIEW" "1" "05/17/2009" "seaview 4.0" "Seaview Manual"
+.TH "SEAVIEW" "1" "05/27/2009" "seaview 4.0" "Seaview Manual"
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
@@ -60,6 +60,8 @@
 \fBclustalw\fR(1)\&.
 .PP
 The home page of SeaView is http://pbil\&.univ\-lyon1\&.fr/software/seaview\&.html\&.
+.PP
+SeaView usees some components of the PHYLIP package, see \(oqhttp://evolution\&.genetics\&.washington\&.edu/phylip\&.html\(cq\&.
 .SH "REFERENCE"
 .PP
 If you use SeaView in a published work, please cite the following reference: Galtier, N\&., Gouy, M\&. and Gautier, C\&. (1996) SeaView and Phylo_win, two graphic tools for sequence alignment and molecular phylogeny\&. Comput\&. Applic\&. Biosci\&., 12, 543\-548\&.
@@ -88,10 +90,10 @@
 .br
 .PP
 SeaView
-is released under the GNU General Public Licence
+is released under the GNU General Public Licence, with a special permission to use some source files from the PHYLIP package\&. Because these files are used, you are not allowed generate revenue with SeaView\&.
 .PP
 You can redistribute and/or modify this manpage under same terms as SeaView itself\&.
 .PP
-On Debian systems, the complete text of the GNU General Public License can be found in
-\fI/usr/share/common\-licenses/GPL\fR\&.
+On Debian systems, the complete text of the GNU General Public License version 2 can be found in
+\fI/usr/share/common\-licenses/GPL\-2\fR\&.
 .sp

Modified: trunk/packages/seaview/trunk/debian/seaview.1.xml
===================================================================
--- trunk/packages/seaview/trunk/debian/seaview.1.xml	2009-05-27 04:24:24 UTC (rev 3438)
+++ trunk/packages/seaview/trunk/debian/seaview.1.xml	2009-05-27 13:22:23 UTC (rev 3439)
@@ -78,11 +78,11 @@
        <holder>Charles Plessy</holder>
      </copyright>
      <legalnotice>
-       <para><application>SeaView</application> is released under the GNU General Public Licence</para>
+       <para><application>SeaView</application> is released under the GNU General Public Licence, with a special permission to use some source files from the PHYLIP package. Because these files are used, you are not allowed generate revenue with SeaView.</para>
        
        <para>You can redistribute and/or modify this manpage under same terms as SeaView itself.<!-- This also applies to this xml document. --></para>
        
-       <para> On Debian systems, the complete text of the GNU General Public License can be found in <filename>/usr/share/common-licenses/GPL</filename>.</para>
+       <para> On Debian systems, the complete text of the GNU General Public License version 2 can be found in <filename>/usr/share/common-licenses/GPL-2</filename>.</para>
      </legalnotice>
   </refentryinfo>
   
@@ -152,6 +152,8 @@
     </para>
     
     <para>The home page of SeaView is http://pbil.univ-lyon1.fr/software/seaview.html.</para>
+    
+    <para>SeaView usees some components of the PHYLIP package, see ‘http://evolution.genetics.washington.edu/phylip.html’.</para>
   </refsect1>
 
   <refsect1>

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